Analysis of the algorithm: From rankings to backup genes.

Ranking section

Table 1. Performance summary for every kernel and net before integration.

Net	Kernel	tpr_down_ci_0.95	tpr_up_ci_0.95	fpr_down_ci_0.95	fpr_up_ci_0.95	f
biological_process	ct	0.0843958712811172	0.117182756527019	0.000337343197135966	0.000708617548572519	0.127833519137867
biological_process	el	0.0127427184466019	0.0254854368932039	0.00402508690707786	0.0112218193990885	0.00521045347227876
biological_process	ka	0.134775349119611	0.170006071645416	0.00045779032189103	0.000789437047867043	0.173853989813243
biological_process	rf	0.0831663630843959	0.117805100182149	0.000356609522935531	0.000721665987087651	0.12778603268945
cellular_component	ct	0.0697815533980582	0.0989077669902913	0.000433386056000642	0.00104318726237029	0.0964673913043478
cellular_component	el	0.0260764099454215	0.0436779866585809	0.0238847873665587	0.0425655399882364	0.00196536884551523
cellular_component	ka	0.070995145631068	0.0989077669902913	0.000449575353299178	0.00114773391515818	0.0987569060773481
cellular_component	rf	0.0582372572815534	0.087378640776699	0.000300602559654239	0.0006481449644122	0.10048231511254
disease	ct	0.346558219178082	0.410291095890411	0.00177350953889026	0.00222690724566255	0.224313725490196
disease	el	0.177397260273973	0.217808219178082	0.00621742159430739	0.00808377977956052	0.0450339296730413
disease	ka	0.28972602739726	0.358921232876712	0.000418001442013708	0.000662596172275005	0.3674228337672
disease	rf	0.344520547945205	0.413013698630137	0.00178274268573532	0.00225071264074084	0.226482213438735
gene_PS	ct	0.21379980563654	0.295432458697765	0.0014734099393209	0.00199233626293962	0.191381065490329
gene_PS	el	0.229571984435798	0.321035992217899	0.000668434471343864	0.00100647651076217	0.292846855496879
gene_PS	ka	0.372568093385214	0.443579766536965	0.00094429108615953	0.00136047680827306	0.331782945736434
gene_PS	rf	0.329766536964981	0.417339494163424	0.00110905186292657	0.00155536526993464	0.302395209580838
gene_TF	ct	0.0285714285714286	0.114285714285714	0.0229543094496366	0.0987839536536044	0.0051907604464054
gene_TF	el	0	0.0214285714285714	0.00276520741105099	0.0350122970978849	0.00472813238770686
gene_TF	ka	0.0428571428571429	0.128571428571429	0.044582991747281	1	0.00450704225352113
gene_TF	rf	0.1	0.214285714285714	0.0625233644859813	0.196682242990654	0.00622259934945552
gene_hgncGroup	ct	0.0883652430044183	0.120784241531664	0.00111448721402568	0.00189872854924986	0.0835975785528971
gene_hgncGroup	el	0.114204126750184	0.156963890935888	0.000864105762922642	0.0013470169702303	0.125613346418057
gene_hgncGroup	ka	0.110537951363301	0.148120854826824	0.000418245302953257	0.000924803120562144	0.155866900175131
gene_hgncGroup	rf	0.0972733971997052	0.133382461311717	0.000725190160902339	0.00132070270612072	0.111072783718524
genetic_interaction_effect_bicor	ct	0.0323785803237858	0.0523038605230386	0.000583144838823794	0.00186037380873256	0.0431519699812383
genetic_interaction_effect_bicor	el	0.00186799501867995	0.00933997509339975	0.000125947385911688	0.002000552083445	0.00932159502848265
genetic_interaction_effect_bicor	ka	0.0330012453300125	0.0529265255292653	0.000427154465443864	0.00106022801582282	0.0520361990950226
genetic_interaction_effect_bicor	rf	0.0323785803237858	0.0523038605230386	0.000585315652369671	0.0017892729650633	0.0431789737171464
molecular_function	ct	0.0557256582976118	0.0826852418860992	0.000410505132369438	0.00112406119375737	0.0845173041894353
molecular_function	el	0.00489596083231334	0.0140758873929009	0.00462627128705035	0.013561147093353	0.00227305014916892
molecular_function	ka	0.0648958971218616	0.0930802204531537	0.000614649651281694	0.00133083072942224	0.0818494220556076
molecular_function	rf	0.0557256582976118	0.0820575627679118	0.000357173761862701	0.0011439400894669	0.0857771260997068
pathway	ct	0.13323124042879	0.203675344563553	0.00138046479364146	0.00257948169460714	0.138707765263782
pathway	el	0.165644171779141	0.237730061349693	0.000486892889544211	0.00104742411065911	0.243816254416961
pathway	ka	0.193251533742331	0.273006134969325	0.000666247503387193	0.00177872450208699	0.250587314017228
pathway	rf	0.159509202453988	0.23159509202454	0.00073980040765907	0.00143018112295893	0.203519510328998
phenotype	ct	0.212305611899932	0.271129141311697	0.000628617000967606	0.000906350340089529	0.251090970124203
phenotype	el	0.0297128378378379	0.0506756756756757	0.00116914208298939	0.00267455283121653	0.0283687943262411
phenotype	ka	0.225135226504395	0.290060851926978	0.000407976596654473	0.00059830124730221	0.308575803981623
phenotype	rf	0.212288708586883	0.271129141311697	0.000615518335455486	0.000899808441309355	0.250924991590986
protein_interaction	ct	0.259615384615385	0.305288461538462	0.000934940345952621	0.00128462667803673	0.228639618138425
protein_interaction	el	0.260802283653846	0.3197265625	0.00068313464164908	0.000946886152328165	0.280022446689113
protein_interaction	ka	0.26035778713169	0.307276007215875	0.000632959341874322	0.000965050001706543	0.272212790039615
protein_interaction	rf	0.252403846153846	0.300495793269231	0.000797886781680821	0.00106634421608361	0.244357976653696

Table 2. Performance summary for every kernel after integration

Integration	Kernel	tpr_down_ci_0.95	tpr_up_ci_0.95	fpr_down_ci_0.95	fpr_up_ci_0.95	f
integration_mean_by_presence	ct	0.173031026252983	0.220763723150358	0.000637454143310874	0.000889986519979975	0.203863298662704
integration_mean_by_presence	el	0.365373134328358	0.422089552238806	0.000558050999382935	0.000805838569148928	0.377771540836374
integration_mean_by_presence	ka	0.324164179104478	0.372537313432836	0.000296465394887956	0.000511424926637029	0.39986399183951
integration_mean_by_presence	rf	0.256716417910448	0.307462686567164	0.000546266246672955	0.000800709188208784	0.286556603773585
mean	ct	0.24582338902148	0.294152744630072	0.000902245746715143	0.00136495461521416	0.225900681596884
mean	el	0.337313432835821	0.405985074626866	0.000587814232288119	0.000814032755200808	0.367034834324554
mean	ka	0.35044776119403	0.426268656716418	0.000413928218417247	0.000662754487823619	0.424922118380062
mean	rf	0.285955223880597	0.343880597014925	0.000737092041098652	0.00110847204461741	0.283033620015637

Backup Pairs Coverage By Layer Non integrated

Backup Pairs Coverage By Layer Integrated

Distribution of ranks in dataset by non integrated kernels

Distribution of ranks in dataset by Integrated kernels

ROC-AUCs for Non-integrated kernel and layer

ROC-AUCS for integrated kernels

CDF plots of non integrated kernels

ROC plots of non integrated kernels

ROC plots of integrated kernels

CDF plots of integrated kernels